GC/LC

May 09, 2013

Working on poorly collected data is not fun. It can be frustrating and time consuming.

A good LC-MS+ TOF dataset is consistent across a peak and exhibits a mass measurement accuracy of < 5 ppm. The TOF data below shows a significant variation across the peak m/z 205.136 to 205.076 to 205.096 (range m/z 205.106 +/- 0.030 Da or 146 ppm). This variation can inhibit the determination of a concrete molecular formula and increase false positives. The variation can be a result of bad calibrations or issues with the flight tube.

June 13, 2012

To identify co-eluting components on a chromatogram, one searches for any distinct differences between the components.

There are basically three criteria to check the XICs (extracted ion chromatograms) for to confirm whether the m/z signals pertain to the same component: line shape, signal apex and retention time range. The XICs for m/z 188.1 and 205.1 show a similar line shape, a common apex and a comparable retention time range. Based on these three matches, the m/z 188.1 and 205.1 are most likely related to the same component.

However, we cannot rule out the case for co-elution of a binary mixture at 2.86 minutes. The lack of any differences from the XICs suggests two plausible explanations, either m/z 188.1 and 205.1 are part of the same component or there is a 'perfect' co-elution between the two components.

June 05, 2012

Sorting out what compounds are present in a mixture is a difficult task. The process is further complicated when the compounds co-elute on a chromatographic run.

An LC/MS (ESI+) was collected for an unknown sample comprising of small organic molecules. The total ion chromatogram (TIC shown in black) shows a signal at 2.86 minutes. The extracted ion chromatograms (XICs) for m/z 188.1 (red) and 205.1 (green) appear at 2.86 minutes. Are the signals related to the same component? Or is co-elution occurring?

December 05, 2011

The explanation offered herein covers one possible scenario to a complicated situation. Please note that other explanations are possible.

The LC/MS data shows an unknown at 1.8 minutes exhibiting an [M+H]+ at m/z 260 and an [M-H]- at m/z 256. The difference of 4 mass units lends itself into a scenario of conflicting data.

One potential explanation for the differing LC/MS data is the unknown is a really comprised of a mixture of two compounds ionizing under separate ion modes and differing by 2 mass units. The short column run (< 2.5 minutes) done under UPLC conditions appears not to be adequate to separate out the mixture as they elute.

November 23, 2011

The purpose of this puzzle is to examine data collected from multiple detectors with the hopes of sorting out the conflicting data surrounding the unknown.

In an attempt to identify the structure for an unknown, UPLC data was collected using a C18 column with a run time of 2.2 minutes. The UV, ESI- and ESI+ traces are presented for the unknown eluting at 1.8 minutes. What is the mass of the unknown?

May 04, 2010

Part 1 presented a challenge to determine an experiment to distinguish two very similar products from each other, namely 3-methyl-5-(pyridin-2-yloxy)pyridine and 5'-methyl-2H-1,3'-bipyridin-2-one. The products have identical formula weights and the LC/MS and 1H NMR are too similar to draw any conclusion from.

The first step is to determine what is different between the two products and then identify an experiment specifically designed to focus on that difference. The obvious difference between the two products is the position of the oxygen atom—an ester group verse a carbonyl group. An FT-IR experiment, as commented by the reader Felipe A., can be used to sort out the products.

Other experiments can include the use of reducing agents, 15N NMR, 1H -13C HMBC, 1D NOE, 1H-1H TOCSY, MS2, etc. Note free water, acids and sample concentration can inhibit the use of some of these experiments.

A 13C NMR experiment may appear to be another good choice when trying to identify a carbonyl group. However, the carbonyl is part of a conjugated system and so the 13C chemical shift is expected around 160 ppm, which also happens to be expected for the 13C chemical shift of the O-C=N group on the other product.

April 28, 2010

Many organic chemists—if not all—check to see if a synthetic reaction is complete via TLC and LC/MS and/or 1H NMR. At the same time, the chemists are using the analytical data to verify that the final product is what they intended on making. In some cases, LC/MS and 1H NMR do not adequately distinguish one potential product from another. It then becomes a question of identifying a technique(s) that can clearly verify the correct product.

The chemical structures shown below (3-methyl-5-(pyridin-2-yloxy)pyridine and 5'-methyl-2H-1,3'-bipyridin-2-one) are two possible products for a synthetic reaction. They have an identical formula weight (FW) and a nearly identical MS and 1H NMR (not shown). What other experiments can a chemist/spectroscopist propose that will assist in identifying the correct structure and thus distinguish the ester from the carbonyl product?

I would like to give a special thanks to David C. Adams for proposing the idea.

March 02, 2010

Whenever a GC column is used to identify and/or quantify a sample, the column stationary phase can bleed into the MS source along with the sample. High column bleed can hinder the analysis of a sample. The resulting spectral interference typically manifests itself as discrete peaks and/or an increase in the drift of the baseline, which in turn, produces data with low signal-to-noise and poor sensitivity.

The GC-EI mass spectra below are two examples showing high column bleed. The ion peaks at m/z 73, 133, 193, 207, 267, 281, 355 and 429 are not part of the purified sample but pertain to the column stationary phase. The major column bleed ion, m/z 207, is a result of the formation of hexamethylcyclotrisiloxane. The presence of these characteristic masses for siloxanes indicates there is a significant column bleed and that the column may need replacing.

January 20, 2010

TLC (Thin Layer Chromatography) offers a simple approach to identifying a solvent(s) for separating out a mixture, monitoring a reaction to completion, etc. Furthermore, the TLC plates can be stained to identify the presence or absence of various functional groups such as amines, ketones, etc. This qualitative experiment does offer various drawbacks.

The process of staining typically requires the items shown in the illustration below.

The following websites offer more insight into the process of staining.

January 04, 2010

The line shape of a peak on a chromatogram can offer some insight into the presence of a functional group. However, issues with the instrument are also known to affect the line shape for a peak.

The GC/MS EI+ Total Ion Chromatogram/Current (TIC) below shows five peaks. All of the peaks with the exception of the peak at 1.8 minutes exhibit a symmetrical line shape. The asymmetry of the peak at 1.8 minutes is typical for a structure containing an acidic group (i.e. -COOH).